Markers + reference

Fallopia

4 species · Polygonaceae · Caryophyllales

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Species 4
Genome length 163–165 kb
Candidate markers 270
Primer pairs 110

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1472 0.0590 0.67 71.6 yes View details
trnS-GCU-trnG-UCC LSC 1185 0.0499 0.66 76.6 yes View details
rpoB-trnC-GCA LSC 1361 0.0387 0.94 74.6 yes View details
petN-psbM LSC 1094 0.0478 0.96 81.3 yes View details
trnE-UUC-trnT-GGU LSC 914 0.0442 0.97 79.6 yes View details
trnT-GGU-psbD LSC 1497 0.0349 0.93 74.9 yes View details
accD LSC 1515 0.0364 0.99 70.5 yes View details
ycf4-cemA LSC 890 0.0474 0.95 82.8 yes View details
psaJ-rpl33 LSC 541 0.0569 0.96 80.8 yes View details
ndhF-rpl32 SSC 1083 0.0480 0.89 80.6 yes View details
rpl32-trnL-UAG SSC 745 0.0499 0.99 82.1 yes View details
ndhA SSC 2242 0.0268 0.99 63.2 yes View details
trnW-CCA-trnP-UGG LSC 296 0.0574 1.00 82.6 yes View details
trnC-GCA-petN LSC 767 0.0369 0.98 78.6 yes View details
ycf3-trnS-GGA LSC 943 0.0394 0.97 77.6 yes View details
rps18-rpl20 LSC 225 0.0751 0.94 77.5 yes View details
rpoA-rps11 LSC 76 0.0504 1.00 77.5 yes View details
petG-trnW-CCA LSC 107 0.0685 1.00 76.1 yes View details
trnV-UAC-trnM-CAU LSC 176 0.0380 0.97 75.6 yes View details
trnM-CAU-atpE LSC 267 0.0453 0.96 75.1 yes View details
psaA-ycf3 LSC 746 0.0366 0.98 74.6 yes View details
atpH-atpI LSC 676 0.0402 0.97 74.5 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT GAGGTTCGAATCCTTCCGTC 1499–1949 1.000 89.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT CTTACAGCAGCTTGCCAAAC 2065–2518 1.000 88.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1659–2114 0.750 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT GATTTTGGCGGGAATTGACG 2067 0.250 49.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT GCGGGAATTGACGAACAATC 2060 0.250 48.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 1007–1308 1.000 59.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA ACGAATCACACTTTTACCACT 977–1278 1.000 58.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 1010–1311 1.000 58.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 1009–1310 1.000 58.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA GAACGAATCACACTTTTACCACT 979–1280 1.000 57.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TGCTCGGAATCCACAAACAA 1264–1282 1.000 85.0
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT TGCTCGGAATCCACAAACAA 1347–1365 1.000 84.6
atpH-atpI_p3 atpH-atpI CCTCGTATTTTCCCCTCTGC TGCTCGGAATCCACAAACAA 1384–1402 1.000 84.5
atpH-atpI_p4 atpH-atpI CCTCATCCTCAAATCAGCCC TATCGTCCTTGGGTTCCCTT 1523–1534 1.000 84.4
atpH-atpI_p5 atpH-atpI CCTCATCCTCAAATCAGCCC TGCTCGGAATCCACAAACAA 1623–1634 1.000 84.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GCCCAGGTATTGTCGACATT ACTCGGGGTTACTGAACAGA 1828–1906 1.000 89.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAACCCCGCGGATA ACTCGGGGTTACTGAACAGA 2049–2127 1.000 88.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT ACTCGGGGTTACTGAACAGA 2297–2375 1.000 88.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCAAATTAACCCCGCGGATA CGAATCAAGCGCGTATCAAC 1710–1789 0.750 77.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CGAATCAAGCGCGTATCAAC 1958–2037 0.750 77.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG CCATACGACGAGTGAAAGGG 848–868 1.000 86.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG CCCATACGACGAGTGAAAGG 849–869 1.000 86.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG CCCCATACGACGAGTGAAAG 850–870 1.000 86.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG AGCCCAAGCGAGACTTACTA 803–823 1.000 86.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG ACGACGAGTGAAAGGGAAAA 844–864 1.000 82.4
petN-psbM_p1 petN-psbM TCTGTTCAGTAACCCCGAGT CGGCGAAGTGATTTGATAGC 1805–1880 1.000 83.7
petN-psbM_p2 petN-psbM CCTTTCACTCGTCGTATGGG CGGCGAAGTGATTTGATAGC 1395–1480 1.000 83.6
petN-psbM_p3 petN-psbM CGTCGTATGGGGAAGAAGTG CGGCGAAGTGATTTGATAGC 1386–1471 1.000 83.6
petN-psbM_p4 petN-psbM CTTTCACTCGTCGTATGGGG CGGCGAAGTGATTTGATAGC 1394–1479 1.000 83.6
petN-psbM_p5 petN-psbM AATTGCGGGTAAGAATCCCC CGGCGAAGTGATTTGATAGC 1558–1643 1.000 83.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Fallopia ciliinervis ON229561.1 164871 View on NCBI ↗
Fallopia convolvulus NC_082245.1 162540 View on NCBI ↗
Fallopia dentatoalata NC_082246.1 162617 View on NCBI ↗
Fallopia dumetorum NC_082247.1 162771 View on NCBI ↗